Name: Rhodothermus profundi 2037 Souchothèque de Bretagne
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 17795

Type strain:

Species: Rhodothermus profundi

Strain Designation: 2037 Souchothèque de Bretagne

Culture col. no.: DSM 22212, JCM 15944, PRI 2902

Strain history: J.-L. Birrien PRI 2902.

NCBI tax ID(s): 633813 (species)

SI-ID 398419

DSM 22212

Special Collections

Section

Rhodothermus profundi 2037 Souchothèque de Bretagne is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from hydrothermal chimney material.

Gram-negative
rod-shaped
aerobe
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Rhodothermota*
	Class	*Rhodothermia*
	Order	*Rhodothermales*
	Family	*Rhodothermaceae*
	Genus	*Rhodothermus*
	Species	**Rhodothermus profundi**
	Full Scientific Name (LPSN)	Rhodothermus profundi Marteinsson et al. 2010

Information on morphological and physiological properties Morphology

[Ref.: #29418]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %90.87

[Ref.: #29418]	Cell length	1.5-3.5 µm

[Ref.: #29418]	Cell width	0.5 µm

[Ref.: #29418]	Cell shape	rod-shaped

[Ref.: #29418]	Motility	no

[Ref.: #29418]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16205]

Culture medium

HALF STRENGTH BACTO MARINE BROTH (DSMZ Medium 514a)

[Ref.: #16205]

Culture medium growth

[Ref.: #16205]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16205]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #16205]	growth	70 °C
[Ref.: #29418]	growth	55-80 °C
[Ref.: #29418]	optimum	70 °C
[Ref.: #67770]	growth	70 °C

	pH	Kind of pH		pH
[Ref.: #29418]			optimum	7
[Ref.: #29418]			growth	06-08

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29418]

Oxygen tolerance

aerobe

[Ref.: #29418]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29418]		NaCl		growth	01-05	%
[Ref.: #29418]		NaCl		optimum	02-03	%

[Ref.: #29418]	Observation	aggregates in chains
[Ref.: #67770]	Observation	quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29418]	asparagine ChEBI	+	carbon source
[Ref.: #29418]	aspartate ChEBI	+	carbon source
[Ref.: #29418]	gelatin ChEBI	+	carbon source
[Ref.: #29418]	glutamate ChEBI	+	carbon source
[Ref.: #29418]	pyruvate ChEBI	+	carbon source

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #29418]		catalase	+	1.11.1.6

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #16205]	Sample type/isolated from	hydrothermal chimney material
[Ref.: #16205]	Geographic location (country and/or sea, region)	East Pacific Rise, hydrothermal vent fields of Genesis (12.449844° N 103.56812° W) at a depth of 2634 m
[Ref.: #16205]	Geographic location	12.4498°/-103.5680°

[Ref.: #67770]	Sample type/isolated from	Chimney collected from a deep-sea hydrothermal field at a depth of 2,634 m on the East Pacific Rise
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Hydrothermal vent
#Condition	#Thermophilic (>45°C)	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence FJ624399 (>99% sequence identity) for Rhodothermus profundi from Microbeatlas

Aquatic Samples	12
Soil Samples	4
Animal Samples	6
Plant Samples	2
Total Samples	24

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #16205]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #16205]	Rhodothermus profundi strain PRI 2902 16S ribosomal RNA gene, partial sequence	FJ624399	1509	GenBank ENA	633813 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Rhodothermus profundi DSM 22212	GCA_900142415	scaffold	GenBank ENA	633813 tax ID
[Ref.: #66792]	Rhodothermus profundi strain DSM 22212	633813.3	wgs	PATRIC	633813 tax ID	*
[Ref.: #66792]	Rhodothermus profundi DSM 22212	2622736637	draft	JGI IMG/M	633813 tax ID	*

[Ref.: #16205]	GC-content	60.9 mol%	high performance liquid chromatography (HPLC)
[Ref.: #29418]	GC-content	60.9 mol%
[Ref.: #67770]	GC-content	60.7 mol%	high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Rhodothermus profundi DSM 22212 NCBI: GCA_900142415.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	87	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rhodothermus profundi strain DSM 22212 PATRIC: 633813.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	90.87	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	83.181	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	82.199	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	69.089	no
[Ref.: #69480]	thermophilic	thermophileⓘ	yes	63.615	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	51.852	no

Availability in culture collections External links

[Ref.: #16205]

Culture collection no.

DSM 22212, JCM 15944, PRI 2902

[Ref.: #86787]

SI-ID 398419

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rhodothermus bifroesti sp. nov., a thermophilic bacterium isolated from the basaltic subsurface of the volcanic island Surtsey.	Bergsten P, Vannier P, Mougeolle A, Rigaud L, Marteinsson VT	Int J Syst Evol Microbiol	10.1099/ijsem.0.005214	2022	*
Phylogeny	Rhodothermus profundi sp. nov., a thermophilic bacterium isolated from a deep-sea hydrothermal vent in the Pacific Ocean.	Marteinsson VT, Bjornsdottir SH, Bienvenu N, Kristjansson JK, Birrien JL	Int J Syst Evol Microbiol	10.1099/ijs.0.012724-0	2010	*

References

#16205

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22212

#20215

Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#29418

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #25825 (see below)

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#69479

João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#86787

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID398419.1 )

#25825

IJSEM 2729 2010 ( DOI 10.1099/ijs.0.012724-0 , PubMed 20061490 )

* These data were automatically processed and therefore are not curated

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Rhodothermus profundi DSM 22212

Rhodothermus profundi strain DSM 22212

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